chemistry: Add plumed.

* guix-science/packages/chemistry.scm (plumed): New variable.

1 files changed, 57 insertions, 2 deletions

diff --git a/guix-science/packages/chemistry.scm b/guix-science/packages/chemistry.scm
index 7b48278..069e66a 100644
--- a/guix-science/packages/chemistry.scm
+++ b/guix-science/packages/chemistry.scm
@@ -11,14 +11,15 @@
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
-  #:use-module (gnu packages python)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages wget)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages wget)
   #:use-module (guix-science packages fortran))
 
 (define-public wannier90
@@ -138,6 +139,60 @@ programming languages and frameworks (Fortran, C, Python C bindings,
 Python/Numpy, Python/Tensorflow).")
     (license license:mpl2.0)))
 
+(define-public plumed
+  (package
+    (name "plumed")
+    (version "2.10.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/plumed/plumed2")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256 (base32 "1n49dd8rnklflxnyfsn5l7k49xi2ncsvfqvd8v0b4vydwnxzqmb8"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         (string-append "CXX=" #$(this-package-input "openmpi") "/bin/mpic++")
+         (string-append "LDFLAGS=-lopenblas")
+         (string-append "MPIEXEC=" #$(this-package-input "openmpi") "/bin/mpirun")
+         ;; Fix runpath validation error.
+         "--enable-rpath")
+      ;; Prevent non reproducible timeouts.
+      #:parallel-tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'mpi-setup #$%openmpi-setup)
+          (add-before 'check 'fix-tests
+            (lambda _
+              (for-each delete-file-recursively
+                        ;; Need missing data.
+                        '("regtest/basic/rt-make-7"
+                          "regtest/basic/rt-make-subprocess"
+                          "regtest/basic/rt-vimsyntax"
+                          ;; Need too much resources to pass on CI.
+                          "regtest/basic/rt-NeigbourlistInitializationError")))))))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list fftw
+           gsl
+           openmpi
+           openblas
+           zlib))
+    (home-page "https://www.plumed.org/")
+    (synopsis "The community-developed PLUgin for MolEcular Dynamics")
+    (description "PLUMED is a library that provides a wide range of different methods,
+which include: enhanced-sampling algorithms, free-energy methods,
+tools to analyze the vast amounts of data produced by molecular
+dynamics (MD) simulations.  These techniques can be used in combination
+with a large toolbox of collective variables that describe complex
+processes in physics, chemistry, material science, and biology.")
+    (license license:lgpl3+)))
+
 (define-public quantum-espresso
   (package
     (name "quantum-espresso")